Top

Published in:

01-02-2016 | Brief Report

Bioinformatics analysis of codon usage patterns and influencing factors in Penaeus monodon nudivirus

Authors: Anuj Tyagi, Niraj K. Singh, Volker Gurtler, Indrani Karunasagar

Published in: Archives of Virology | Issue 2/2016

Abstract

Penaeus monodon nudivirus (PmNV) is one of the most important and most commonly reported shrimp viruses. In the present study, codon usage of PmNV was studied in detail. Based on effective number of codons (ENC) values, strong to low codon usage bias was observed in PmNV genes. Nucleotide composition–ENC correlation analysis and the GC3 versus ENC relationship indicated that compositional constraint has a major effect on codon usage of PmNV. At the whole-genome level, relative synonymous codon usage (RSCU) analysis showed almost complete antagonism between the codon usage pattern of PmNV and its host P. monodon. However, codon adaptive index (CAI) values indicated that forces of selective/translational constraints have been able to overcome this antagonism in some genes.

Available only for authorised users

Flegel TW, Lightner DV, Lo CF, Owens L (2008) Shrimp disease control: past, present and future. In: Bondad-Reantaso MG, Mohan CV, Crumlish M, Subasinghe RP (eds) Diseases in Asian aquaculture VI. Fish Health Section, Asian Fisheries Society, Manila, Philippines, pp 355–378

Rajendran KV, Makesh M, Karunasagar I (2012) Monodon baculovirus of shrimp. Indian J Virol 23:149–160PubMedCentralCrossRefPubMed

Flegel TW (2012) Historic emergence, impact and current status of shrimp pathogens in Asia. J Invertebr Pathol 110:166–173CrossRefPubMed

Lightner DV, Redman RM, Bell TA (1983) Observation on the geographic distribution, pathogenesis and morphology of the baculovirus from Penaeus monodon Fabricius. Aquaculture 32:209–233CrossRef

Thikiew N (1990) A serious MBV outbreak in the black tiger prawn. Livest Prod Mag 7:13–16

Sharp PM, Matassi G (1994) Codon usage and genome evolution. Curr Opin Genet Dev 4:851–860CrossRefPubMed

Plotkin JB, Kudla G (2011) Synonymous but not the same: the causes and consequences of codon bias. Nat Rev Genet 12:32–42PubMedCentralCrossRefPubMed

Butt AM, Nasrullah I, Tong Y (2014) Genome-wide analysis of codon usage and influencing factors in chikungunya viruses. PLoS One 9:e90905PubMedCentralCrossRefPubMed

Roychoudhury S, Mukherjee D (2010) A detailed comparative analysis on the overall codon usage pattern in herpesviruses. Virus Res 148:31–43CrossRefPubMed

10.

Sablok G, Sánchez-Paz A, Wu X, Ranjan J, Kuo J, Bulla I (2012) Genome dynamics in three different geographical isolates of white spot syndrome virus (WSSV). Arch Virol 157:2357–2362CrossRefPubMed

11.

Yang YT, Lee DY, Wang Y, Hu JM, Li WH, Leu JH, Chang GD, Ke HM, Kang ST, Lin SS, Kou GH, Lo CF (2014) The genome and occlusion bodies of marine Penaeus monodon nudivirus (PmNV, also known as MBV and PemoNPV) suggest that it should be assigned to a new nudivirus genus that is distinct from the terrestrial nudiviruses. BMC Genomics 15:628PubMedCentralCrossRefPubMed

12.

Sharp PM, Cowe E (1991) Synonymous codon usage in Saccharomyces cerevisiae. Yeast 7:657–678CrossRefPubMed

13.

Wright F (1990) The ‘effective number of codons’ used in a gene. Gene 87:23–29CrossRefPubMed

14.

Sharp PM, Tuohy TM, Mosurski KR (1986) Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes. Nucleic Acids Res 14:5125–5143PubMedCentralCrossRefPubMed

15.

Sharp PM, Li WH (1987) The codon Adaptation Index–a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res 15:1281–1295PubMedCentralCrossRefPubMed

16.

Puigbò P, Bravo IG, Garcia-Vallve S (2008) CAIcal: a combined set of tools to assess codon usage adaptation. Biol Direct 3:38PubMedCentralCrossRefPubMed

17.

Puigbò P, Bravo IG, Garcia-Vallvé S (2008) E-CAI: a novel server to estimate an expected value of Codon Adaptation Index (eCAI). BMC Bioinformatics 9:65PubMedCentralCrossRefPubMed

18.

Greenacre M (1984) Theory and applications of correspondence analysis. Academic Press, London

19.

Sueoka N (1988) Directional mutation pressure and neutral molecular evolution. Proc Natl Acad Sci U S A 85:2653–2657PubMedCentralCrossRefPubMed

20.

Das S, Paul S, Dutta C (2006) Synonymous codon usage in adenoviruses: influence of mutation, selection and protein hydropathy. Virus Res 117:227–236CrossRefPubMed

21.

Zhang Y, Liu Y, Liu W, Zhou J, Chen H, Wang Y, Ma L, Ding Y, Zhang J (2011) Analysis of synonymous codon usage in hepatitis A virus. Virol J 8:174PubMedCentralCrossRefPubMed

22.

Deka H, Chakraborty S (2014) Compositional Constraint Is the Key Force in Shaping Codon Usage Bias in Hemagglutinin Gene in H1N1 Subtype of Influenza A Virus. Int J Genomics 2014:349139PubMedCentralCrossRefPubMed

23.

Jiang P, Sun X, Lu Z (2007) Analysis of synonymous codon usage in Aeropyrum pernix K1 and other Crenarchaeota microorganisms. J Genet Genomics 34:275–284CrossRefPubMed

24.

Rohrmann GF (1992) Baculovirus structural proteins. J Gen Virol 73(Pt 4):749–761CrossRefPubMed

25.

Ramasamy P, Rajan PR, Purushothaman V, Brennan GP (2000) Ultrastructure and pathogenesis of Monodon baculovirus (Pm SNPV) in cultural larvae and natural brooders of Penaeus monodon. Aquaculture 184:45–66CrossRef

26.

Boonsanongchokying C, Sang-oum W, Sithigorngul P, Sriurairatana S, Flegel TW (2006) Production of monoclonal antibodies to polyhedrin of monodon baculovirus (MBV) from shrimp. ScienceAsia 32:371–376CrossRef

27.

Wang Y, Bininda-Emonds OR, van Oers MM, Vlak JM, Jehle JA (2011) The genome of Oryctes rhinoceros nudivirus provides novel insight into the evolution of nuclear arthropod-specific large circular double-stranded DNA viruses. Virus Genes 42:444–456CrossRefPubMed

28.

Rohrmann GF (2011) Baculovirus molecular biology. Bethesda (MD): National library of medicine (US), National center for biotechnology information http://www.ncbi.nlm.nih.gov/books/NBK49500/

29.

Sánchez G, Bosch A, Pintó RM (2003) Genome variability and capsid structural constraints of hepatitis a virus. J Virol 77:452–459PubMedCentralCrossRefPubMed

30.

Mueller S, Papamichail D, Coleman JR, Skiena S, Wimmer E (2006) Reduction of the rate of poliovirus protein synthesis through large-scale codon deoptimization causes attenuation of viral virulence by lowering specific infectivity. J Virol 80:9687–9696PubMedCentralCrossRefPubMed

31.

Hu JS, Wang QQ, Zhang J, Chen HT, Xu ZW, Zhu L, Ding YZ, Ma LN, Xu K, Gu YX, Liu YS (2011) The characteristic of codon usage pattern and its evolution of hepatitis C virus. Infect Genet Evol 11:2098–2102CrossRefPubMed

32.

Gouy M, Gautier C (1982) Codon usage in bacteria: correlation with gene expressivity. Nucleic Acids Res 10:7055–7074PubMedCentralCrossRefPubMed

33.

Sharp PM, Li WH (1986) Codon usage in regulatory genes in Escherichia coli does not reflect selection for ‘rare’ codons. Nucleic Acids Res 14:7737–7749PubMedCentralCrossRefPubMed

Title: Bioinformatics analysis of codon usage patterns and influencing factors in Penaeus monodon nudivirus
Authors: Anuj Tyagi
Niraj K. Singh
Volker Gurtler
Indrani Karunasagar
Publication date: 01-02-2016
Publisher: Springer Vienna
Published in: Archives of Virology / Issue 2/2016
Print ISSN: 0304-8608
Electronic ISSN: 1432-8798
DOI: https://doi.org/10.1007/s00705-015-2689-3

ACC 2024 Congress Coverage

Heart Failure Video

At a glance: The ONWARDS insulin icodec trials

Springer Medicine

Bioinformatics analysis of codon usage patterns and influencing factors in Penaeus monodon nudivirus

Abstract

ACC 2024 Congress Coverage

Year in Review: Heart failure and cardiomyopathies

Semaglutide benefits people with type 2 diabetes and obesity-related heart failure

Incentivised to exercise

New intervention for STEMI-related cardiogenic shock

» View more highlights on the ACC 2024 congress hub page

At a glance: The ONWARDS insulin icodec trials

Springer Medicine

Abstract

Please log in to get access to this content

Other articles of this Issue 2/2016

Phylogenetic and biological characterization of three K1203 (H5N8)-like avian influenza A virus reassortants in China in 2014

Single-step concentration and purification of adenoviruses by coxsackievirus-adenovirus receptor-binding capture and elastin-like polypeptide-mediated precipitation

Isolation and sequence analysis of the complete NS1 and VP2 genes of canine parvovirus from domestic dogs in 2013 and 2014 in China

Pseudorabies in farmed foxes fed pig offal in Shandong province, China

Genomic characterization of Ralstonia solanacearum phage ϕRS138 of the family Siphoviridae

Diversity and evolutionary history of lettuce necrotic yellows virus in Australia and New Zealand

ACC 2024 Congress Coverage

Year in Review: Heart failure and cardiomyopathies

Semaglutide benefits people with type 2 diabetes and obesity-related heart failure

Incentivised to exercise

New intervention for STEMI-related cardiogenic shock

» View more highlights on the ACC 2024 congress hub page